The present day Church of St Thomas was constructed in the early 1800s and was built on the site of an earlier church (1722) dedicated to the Primate ‘Thomas’ Lindsay of Armagh from which it derives its name. The site traces its ecclesiastical history back to an ancient church building founded here by St Comgall of Bangor in 580 AD.

Comgall was born in 510 AD on the shore of Larne Lough, he served as a soldier in the army of Dalriada before becoming a Christian, he then entered Clonnard monastery and later Clonmacnoise to study. He dedicated his life to the spreading Christianity and was responsible for the founding of Bangor Abbey of which he was the Abbot in the mid 550 AD. A monastic settlement was established and developed here on Raghery under the auspices of Bangor Abbey 700 and 1000 AD. It was subsequently raided by Vikings on two occasions (790 and 973 AD) and finally destroyed during a raid in 1038 AD. The Vikings may have established a base here at sometime, certainly they would have over wintered here, the evidence of a Viking burial site would also suggest this.

The earliest gravestone dates to 1665 and is that of James Boyd, the son of Andrew, Bishop of Lismore and his wife Christine Campbell, though burials would have occurred a lot earlier. It is an interesting graveyard with a mixture of religion and race including those of sailors washed ashore from HMS Racoon and HMS Viknor.

One name that is very prominent in the church and churchyard is Gage, the family acquired Raghery through John Gage who bought the island for £1750 in 1746 from Alexander MacDonnell, the 5th Earl of Antrim (Lord Antrim) , at the time John Gage was also the Prebendary of the church. This association with the family continued in 1824 when Robert Gage, who owned Raghery, became the curate and then rector.